Quantitative trait loci (QTL) mapping approaches rely on the correct ordering of molecular markers along the chromosomes, which can be obtained from genetic linkage maps or a reference genome sequence. For apple (Malus domestica Borkh), the genome sequence v1 and v2 could not meet this need; therefore, a novel approach was devised to develop a dense genetic linkage map, providing the most reliable marker-loci order for the highest possible number of markers. The approach was based on four strategies: (i) the use of multiple full-sib families, (ii) the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism (SNP) markers, (iii) the construction of a single backcross-type data set including all families, and (iv) a two-step map generation procedure based on the sequential inclusion of markers. The map comprises 15&thinsp;417 SNP markers, clustered in 3&thinsp;K HaploBlock markers spanning 1&thinsp;267&thinsp;cM, with an average distance between adjacent markers of 0.37&thinsp;cM and a maximum distance of 3.29&thinsp;cM. Moreover, chromosome 5 was oriented according to its homoeologous chromosome 10. This map was useful to improve the apple genome sequence, design the Axiom Apple 480&thinsp;K SNP array and perform multifamily-based QTL studies. Its collinearity with the genome sequences v1 and v3 are reported. To our knowledge, this is the shortest published SNP map in apple, while including the largest number of markers, families and individuals. This result validates our methodology, proving its value for the construction of integrated linkage maps for any outbreeding species.

Mentions:
The 21 bi-parental genetic maps already led to the identification of many regions where the genetic and physical maps deviate from collinearity. The final iGLMap allowed for visualization of inconsistencies with version v1 and v3 of the apple genome36 (Figure 4). The most used version is v1, which consists of a Primary Assembly and various alternative scaffold sequences (Figure 4a) representing homologous and possibly also some homoeologous sequences. Genetic data suggests the presence of some inverted regions that can be recognized by short lines at a right angle to the main curve of each graph in Figure 4a, which goes from the bottom-left to the top-right. Two examples are approximately at 20 cM on LG10 and at 35 cM on LG11. The short sequences of dots clearly aligned above or below the main curve represents regions where the position on the genome sequence may be shifted (that is, approximately at 80 cM on LG10, at 75 cM on LG11 and at 60 cM on LG14). Some regions of the iGLMap have their sequence counterparts on non-corresponding pseudo-chromosomes. For example, the initial part of LG1 and the 22–34 cM region of LG10 include markers belonging to other nine pseudo-chromosomes according to the genome sequence; also, the initial region of LG4 (0–10 cM) consists almost entirely of markers from the pseudo-chromosome 9. Alternative scaffold sequences may also combine information from multiple pseudo-chromosomes. For example, the alternative scaffold on pseudo-chromosome 9 seems to contain, for the 20 Mb region, a small fragment of its homoeologous region on LG17.

Mentions:
The 21 bi-parental genetic maps already led to the identification of many regions where the genetic and physical maps deviate from collinearity. The final iGLMap allowed for visualization of inconsistencies with version v1 and v3 of the apple genome36 (Figure 4). The most used version is v1, which consists of a Primary Assembly and various alternative scaffold sequences (Figure 4a) representing homologous and possibly also some homoeologous sequences. Genetic data suggests the presence of some inverted regions that can be recognized by short lines at a right angle to the main curve of each graph in Figure 4a, which goes from the bottom-left to the top-right. Two examples are approximately at 20 cM on LG10 and at 35 cM on LG11. The short sequences of dots clearly aligned above or below the main curve represents regions where the position on the genome sequence may be shifted (that is, approximately at 80 cM on LG10, at 75 cM on LG11 and at 60 cM on LG14). Some regions of the iGLMap have their sequence counterparts on non-corresponding pseudo-chromosomes. For example, the initial part of LG1 and the 22–34 cM region of LG10 include markers belonging to other nine pseudo-chromosomes according to the genome sequence; also, the initial region of LG4 (0–10 cM) consists almost entirely of markers from the pseudo-chromosome 9. Alternative scaffold sequences may also combine information from multiple pseudo-chromosomes. For example, the alternative scaffold on pseudo-chromosome 9 seems to contain, for the 20 Mb region, a small fragment of its homoeologous region on LG17.

Quantitative trait loci (QTL) mapping approaches rely on the correct ordering of molecular markers along the chromosomes, which can be obtained from genetic linkage maps or a reference genome sequence. For apple (Malus domestica Borkh), the genome sequence v1 and v2 could not meet this need; therefore, a novel approach was devised to develop a dense genetic linkage map, providing the most reliable marker-loci order for the highest possible number of markers. The approach was based on four strategies: (i) the use of multiple full-sib families, (ii) the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism (SNP) markers, (iii) the construction of a single backcross-type data set including all families, and (iv) a two-step map generation procedure based on the sequential inclusion of markers. The map comprises 15&thinsp;417 SNP markers, clustered in 3&thinsp;K HaploBlock markers spanning 1&thinsp;267&thinsp;cM, with an average distance between adjacent markers of 0.37&thinsp;cM and a maximum distance of 3.29&thinsp;cM. Moreover, chromosome 5 was oriented according to its homoeologous chromosome 10. This map was useful to improve the apple genome sequence, design the Axiom Apple 480&thinsp;K SNP array and perform multifamily-based QTL studies. Its collinearity with the genome sequences v1 and v3 are reported. To our knowledge, this is the shortest published SNP map in apple, while including the largest number of markers, families and individuals. This result validates our methodology, proving its value for the construction of integrated linkage maps for any outbreeding species.